Coyote Bar And Grill Taco Tuesday, Sandlot Scout Team 2023, Steve Hansen Ex Wife, Articles W

I'm having the same error when building my library's documentation with Github Actions (check here). Choosing "no" made a difference. try this install_github("YosefLab/ImpulseDE2"). In my ~/.Renviron I had the following lines (from https://support.rstudio.com/hc/en-us/articles/200488488-Configuring-R-to-Use-an-HTTP-or-HTTPS-Proxy) causing the problem: solved the problem. rev2023.3.3.43278. Sign in 'getOption("repos")' replaces Bioconductor standard repositories, see Not the answer you're looking for? On Windows, this is most easily done via the installr package. @joycekang on which operating system are you installing pkgdown, and what version are you installing (CRAN or GitHub)? Not able to install locfit r package - Stack Overflow RETURN ( when I try to install the package , it returns a message like this: Warning message: There is a package TSA from CRAN. Is there a chance the problem is on my end, mac OSX Catalina? How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? R . By clicking Sign up for GitHub, you agree to our terms of service and I have had the same problem on Mac (R version 3.2.2) and Ubuntu (R version 3.0.2) and in both instances it was resolved simply by running this before the install.packages command. Since this is a large matrix, you may wish to use the data viewer to examine it. The R version is not the issue - I have all of those packages installed under 3.6.2. from the parent directory of DESCRIPTION) e.g. enter citation("edgeR")): To install this package, start R (version For context, this afternoon I had version 5.2.1, received similar errors and decided to upgrade. R. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Author: Yunshun Chen, Aaron TL Lun, Davis J McCarthy, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth, Maintainer: Yunshun Chen , Gordon Smyth , Aaron Lun , Mark Robinson . How would "dark matter", subject only to gravity, behave? Find centralized, trusted content and collaborate around the technologies you use most. Hisat21.1 , SQLlimitoffset ERROR installing EnhancedVolcano in R4.1 - Bioconductor Not the answer you're looking for? '?repositories' for details. limit n n From searching I managed to install RCurl but I still get the bellow error. In the R 3.2.3 (new in 2016) there was a bug, preventing it some times from finding correct package. "After the incident", I started to be more careful not to trip over things. package diamonds is not available (for R version 3.0.0) Can I tell police to wait and call a lawyer when served with a search warrant? To see which repositories R will look in for your package, and optionally select some additional ones. The best answers are voted up and rise to the top, Not the answer you're looking for? To learn more, see our tips on writing great answers. package "makeR" is not available (for version 3.0.2) package dataset is not available (for R version 3.1.1) Please read the posting By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. If so, how close was it? Why do small African island nations perform better than African continental nations, considering democracy and human development? Perhaps you should add the directory containing `fribidi.pc. Will Gnome 43 be included in the upgrades of 22.04 Jammy? Such a relief reading it now! For Ubuntu 20.04 LTS with R 4.1 use commands below to install needed build-dependencies: Thanks for contributing an answer to Ask Ubuntu! The error message from {systemfonts} suggests that you need to install the freetype2 library on your machine: If you don't have homebrew, I would suggest to install it ( https://brew.sh/) and then run brew install freetype from your terminal. package ImpulseDE2 is not available for Bioconductor version '3.14', A version of this package for your version of R might be available elsewhere, For problems with Ubuntu, check the README: This solution worked for me for debian for the package, When I try install.packages('foobarbaz', repos=NULL) I get error " Error in install.packages("pair", repos = NULL) : type == "both" cannot be used with 'repos = NULL'", Thanks for the comment - I think I forgot to write the, This way do solved my problem, but still update my R to the newest version(from. Please what could be a reason for this error? The Cairo package also requires X11/Intrinsic.h from libxt-dev package. CRAN - Package locfit Another possible warnings message you may get when interacting with CRAN mirrors is: Warning: unable to access index for repository Which may indicate the selected CRAN repository is currently be unavailable. Why does Mister Mxyzptlk need to have a weakness in the comics? Try installing: * deb: libfontconfig1-dev (Debian, Ubuntu, etc), If --static freetype2 is already installed, check that, PATH and PKG_CONFIG_PATH contains a --static freetype2.pc file. privacy statement. as described in this SO answer by imanuelc and the Details section of ?install.packages. Can I tell police to wait and call a lawyer when served with a search warrant? apt or yum). Recovering from a blunder I made while emailing a professor, How to tell which packages are held back due to phased updates. The text was updated successfully, but these errors were encountered: I also have similar problem in installing the package in the new R version: Hi both, ImpulseDE2 is currently not available on the newer bioconductor releases, you can still manually install the package: Clone the GitHub repository first into you local target directory and then install the package via "R CMD INSTALL .". installation problem in R4.1.1 Issue #30 YosefLab/ImpulseDE2 package 'Rbbg' is not available (for R version 2.15.2), package is not available (for R version 2.15.2), package doMC NOT available for R version 3.0.0 warning in install.packages, Dependency Rglpk is not available for package fPortfolio. How to fix this error in R while installing packages? Policy. Hello everybody! Will Gnome 43 be included in the upgrades of 22.04 Jammy? Making statements based on opinion; back them up with references or personal experience. There are several reasons why a package may not be available. <@> DNA IlluminaHumanMethylation450k.db BiocManager"is not available". You can select a different mirror with chooseCRANmirror () and try the installation again. To learn more, see our tips on writing great answers. Look at. Did not work for me in installing the package. I got "package is not available", package dataset is not available (for R version 3.1.1), "package rhipe is not available (for R version 3.1.2)", https://cran.r-project.org/src/contrib/Archive/, cran.r-project.org/bin/linux/ubuntu/README, https://support.rstudio.com/hc/en-us/articles/200488488-Configuring-R-to-Use-an-HTTP-or-HTTPS-Proxy, How Intuit democratizes AI development across teams through reusability. For the Nozomi from Shinagawa to Osaka, say on a Saturday afternoon, would tickets/seats typically be available - or would you need to book? Teams. rev2023.3.3.43278. At first I had about 10 errors regarding packages I couldnt install. You are using an older R version (3.6.3) for which not all packages are available. Why do small African island nations perform better than African continental nations, considering democracy and human development? beyond top level package error in relative import. and what would happen then? --N The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup. Restart RStudio and then re-install the main package allowing for it to run through the updates on the dependencies. Here's more info from the error as requested: Edit 2: An exhaustive printout of all errors and messages as requested in comments: When you call install.packages("broom") (or insert package), it appears the message you receive is: Do you want to install from sources the packages which need compilation? Find centralized, trusted content and collaborate around the technologies you use most. Otherwise, you will need to set up Rtools in order to install from source. Maybe I could have tried to update R using updateR(), but I'm afraid that doing so would interfere with my distribution's package manager. installation - How should I deal with "package 'xxx' is not available The workaround is to set repository manually: This solution might break R but here is an easiest solution that works 99% of time. DESeq2 installation Error (ERROR: dependency locfit is not available for package DESeq2), Traffic: 186 users visited in the last hour, User Agreement and Privacy Connect and share knowledge within a single location that is structured and easy to search. Installation instructions to use this Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? AC Op-amp integrator with DC Gain Control in LTspice, Radial axis transformation in polar kernel density estimate, Trying to understand how to get this basic Fourier Series, Difficulties with estimation of epsilon-delta limit proof. package is not available (for R version 2.15.2) Seeing same as @joycekang. Perhaps you don't really want a package. Running the command sudo dpkg-query -l | grep libcairo2-dev also shows that the Cairo package is fully installed. Assuming that it is reasonably compliant with CRAN standards, you can still download it using install.packages; you just have to specify the repository URL. Is the God of a monotheism necessarily omnipotent? r_-csdn This helped me installing a package on a server (i.e. How to view hierarchical package structure in Eclipse package explorer, How to unload a package without restarting R. How to find out which package version is loaded in R? Package bigmemory not installing on R 64 3.0.2, package "makeR" is not available (for version 3.0.2), package RTN is not available (for R version 3.0.1), package twitterR is not available (for R version 3.1.0), How to install 'Rcpp, package? Ideally, you would update your R installation to the latest version (3.4.3). That error simply tells you that broom is not installed. Turns out, the CRAN snapshot they have on the HPC is from Jan. 2018 (almost 2 years old) and indeed pkgdown did not exist then. Differential expression analysis of RNA-seq expression profiles with biological replication. Installation failure or a non-zero exit status #1427 - GitHub Equation alignment in aligned environment not working properly. Well occasionally send you account related emails. I suggest using Hadley Wickham's devtoolspackage. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Can carbocations exist in a nonpolar solvent? By clicking Sign up for GitHub, you agree to our terms of service and Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, R: Installation of several packages had non-zero exit status, Installation of package forecast had non-zero exit status. Edit (04/08/2020): I recently had an issue with a package (XML) reportedly not available for my R version (3.6.3, latest supported on Debian stretch), after an update of the package in CRAN. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that . You signed in with another tab or window. https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, https://stackoverflow.com/questions/1474081/how-do-i-install-an-r-package-from-source. Policy. It may not have a Windows binary due to requiring additional software that CRAN does not have. The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup. Policy. The package is not in the repositories you selected. (Of course, you may need to install.packages("installr") first.). (Yes/no/cancel) to which you have answered yes. My solution is to read the output of dependent packages that are listed in red and identified with issues (e.g., "cannot install"). CREATE FUNCTION getNthHighestSalary(N INT) RETURNS INT Ask Ubuntu is a question and answer site for Ubuntu users and developers. Unable to install TSA package - General - Posit Forum - RStudio Community Ubuntu and the circle of friends logo are trade marks of Canonical Limited and are used under licence. A concrete example: the latest CRAN version of package rattle for data mining, 5.3.0, does not support R version 3.4 because it had a big update between package versions 5.2.0 (R >= 2.13.0) and 5.3.0 (R >=3.5). AC Op-amp integrator with DC Gain Control in LTspice, Linear Algebra - Linear transformation question. I have tried to install Cairo using the command sudo apt-get install libcairo2-dev but I still get the same error. dependency 'Cairo' is not available for package 'ComplexHeatmap' on I am trying to install DESeq2 and I keep getting errors. Configuration failed to find the --static freetype2 library. 3. ERROR: dependency 'locfit' is not available for package 'DESeq2' locfit1.5-9.2 #R install.packages('https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.2.tar.gz',repos = NULL) 1 2 DEseq2edgeR DEseq2edgeR R , Cannot find xml2-config ERROR: configuration failed for package XML , xml, ERROR: dependency RCurl is not available for package GenomeInfoDb, RCurl, ERROR: dependency locfit is not available for package DESeq2 locfit1.5-9.2, sudo conda , Rpackage xx is not available (for R version xx), internal server error_Rdependencies * are not available for package, #ubuntu centosyum, 'https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.2.tar.gz', RNA, 2016A survey of best practices for RNA-seq data analysisRNATopHat,STARBowtie.TopHatHISAT1. hi I get the following error could you help me please Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. set n=N-1; I know that may sound ridiculous given that your R version is only a couple of years old, but I don't make the rules. In this case, there may be a version in the CRAN (extras) repository (see setRepositories above). install.packages("rlang") I've just updated R to version 3.6.2 "dark and stormy night" released December 12th last year. I run into this error ("package XXX is not available for R version X.X.X") when trying to install pkgdown in my RStudio on my company's HPC. The packages include: broom, tidyr, tidyselect, vctrs, and rlang. Note that when using RStudio, you get this warning as well when installing from another repo than CRAN. Done Building dependency tree Reading state information. Reverse dependencies: Reverse depends: abc, antiProfiles, bumphunter, . As mentioned here (in French), this can happen when you have two versions of R installed on your computer. Typically the lines above "non-zero exit status" indicate what has gone wrong. Using Kolmogorov complexity to measure difficulty of problems? Thanks for contributing an answer to Stack Overflow! I fixed this error on Ubuntu by carefully following the instructions for installing R. This included: For step 1 you can chose any CRAN download mirror in place of my University of Toronto one if you would like. Unfortunately, it seems that I'd have to replicate the process for other packages with non-zero status as well: I wonder if these interdependencies can be resolved within R? CRAN - Package locfit How do I align things in the following tabular environment? locfit: Local Regression, Likelihood and Density Estimation Local regression, likelihood and density estimation methods as described in the 1999 book by Loader. is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: -------------------------- [ERROR MESSAGE] ---------------------------, --------------------------------------------------------------------, ERROR: configuration failed for package systemfonts, * removing /usr/local/lib/R/4.0/site-library/systemfonts, installation of package systemfonts had non-zero exit status, ERROR: dependency systemfonts is not available for package textshaping, * removing /usr/local/lib/R/4.0/site-library/textshaping, installation of package textshaping had non-zero exit status, ERROR: dependencies systemfonts, textshaping are not available for package ragg, * removing /usr/local/lib/R/4.0/site-library/ragg, installation of package ragg had non-zero exit status, ERROR: dependency ragg is not available for package pkgdown, * removing /usr/local/lib/R/4.0/site-library/pkgdown, installation of package pkgdown had non-zero exit status, (converted from warning) installation of package systemfonts had non-zero exit status. That's a bug I reported already a few times, but I don't know if it's sorted already. Follow Up: struct sockaddr storage initialization by network format-string. Asking for help, clarification, or responding to other answers. I don't have any problem resorting to brew, but this does seem a bit off-track. It allows loading package from given directory: Thanks for contributing an answer to Stack Overflow! https://travis-ci.org/github/ramiromagno/gwasrapidd/jobs/740002831. The solution was to find the URL of the compatible version and force install.packages to use it, as follows: This saved me a lot of time debugging what's wrong. How can I use it? and consider updating your R installation to the current version. How to find out which package version is loaded in R? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. You didn't look in the right repository, Next, you should check to see if the package is available.